id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
6641	differences in .cxc execution between 1.1 and 1.4	Eric Pettersen	Tom Goddard	"I've attached a script based on the one from ticket #6624 -- the only difference being omitting ""showAli true"" in the matchmaker command in the attached script.  There are at least three salient differences between execution in 1.1 and 1.4:

1) Rapid Access hides at the start of the script in 1.1

2) Even with Rapid Access hidden, the ""wait"" commands in the script don't cause anything to be drawn in the graphics window in 1.4

3) The final structure colors are noticeably different, possibly due to changes in transparency handling?  Images attached.

The whole rearchitecture of how files get opened changed between 1.1 and 1.2, but I'm not sure how that could affect #2 and #3.
"	defect	closed	moderate		Scenes/Animation		fixed		Elaine Meng Eric Pettersen				all	ChimeraX